Petr Danecek
Petr Danecek
I just added a new option `-a, --anonymize` to https://github.com/pd3/mpileup-tests/blob/main/misc/create-bam-test, which should add a sufficient level of anonymization for most data.
@fd-bnt Thank you, got it and can confirm that it is reproducible. The difference happened between 1.12 and 1.13.
I am thinking if the `+mark-overlaps` plugin would be a good place to add some new functionality to help with this?
That's definitely odd. In the code we have ``` args->n_threads = 0; ... if ( args->n_threads > 0) hts_set_opt(args->out, HTS_OPT_THREAD_POOL, args->files->p); ``` so no threading is done unless set explicitly....
Currently not. An easy workaround would be to add the FORMAT/GT column referring to the alternate alleles and run with `-H I`. I'll mark it as enhancement
You say `bcftools merge` but show `bcftools concat`. When the files can overlap (`concat -a`), all files can have the same coordinate, so there is really no way around keeping...
Mmm, I’m not sure that’s a good idea. Let’s first consider where those thousands of files you want to concatenate are coming from — why are they overlapping in the...
I am happy to accept pull requests, but extremely unlikely to work on this myself.
Thank you for the issue, this is now possible. Note, however, that the change will take effect only after https://github.com/samtools/htslib/pull/1879 is merged
Can you provide a small test case? It is not possible to comment on these specific cases without seeing the data